The fare for the entire journey would be calculated separately (i.e. one fare for the train and one fare for the bus). This is one short coming of the Opal card as it discourages people switching between different modes of transport.
Oh dang.
I misread the 60 min transfer as applying to multiple modes of transport but it isn't.
Although the site can be reasonably (mis)interpreted to be similar to my original one:
A journey consists of one or more trips on eligible services where transfers between services occur within 60 minutes*.
* 60 minutes applies to all services except the Sydney Ferries Manly ferry service where the standard transfer time is 130 minutes from tap on.
https://www.opal.com.au/en/fare-information/trip_journey_and_transfer_explained/
But then here it is clearer:
Using Opal, your fare can be cheaper when making several trips on the same mode of transport, e.g. only ferries, only trains or only buses, if you transfer between services within 60 minutes.
https://www.opal.com.au/en/fare-information/60_minute_transfer/